Make sure that you have the latest update Win2000 Emergency Repair Disk (ERD), Win2000 installation CD, Win2000 boot floppies (if from previous install you found that you need them),
and also Win98 Startup floppy.
It's a very good idea to make a full backup of your partition.
Do you have the same programs installed from Win98 and from Win2K in default directories?
- If YES, better to uninstall updates and such programs itselfs from Win2K if you 100% sure that uninstall works on those programs. Later you will reinstall them.
Or, put notes on those programs and don't touch them from Win98 uninstall.
(As for me, I wouldn't bother and would rather reinstall Win2K from scratch after FDISK /MBR and FORMAT /U)
- If NO, try to uninstall all those programs that installed from Win98 only.
- Delete Windows directory.
- Make sure that you don't touch boot.ini, bootsect.dos, ntldr, ntdetect.com, ntbootdd.sys, hiberfil.sys, pagefile.sys files.
You can try carefully to delete one by one the rest of the stuff you're 100% sure is not in use by Windows 2000.
Update ERD with backing up the registry before every DELETE. Or better to create a new ERD (at least have a couple rotating). Mark the ERD every time about the changes you performed on Win2K.
Restart Win2000 after every DELETE and check how every program works. Restore if something wrong. Empty the Recycle Bin every time after you ensure that everything works fine.
- Finally, you have to backup and then edit boot.ini.
Just a suggestion: next time install every OS on separate partition/drive for multiple boot. It's a good idea and normal common way to have a separate partition for Windows 2000 system itself,
and partition(s) for programs and data.